In 1992, at age 29, he was elected as Mayor of San Juan, becoming the youngest elected mayor in the Philippines at that time. He spearheaded various projects and programs for the improvement of San Juan in the form of - construction of modernized Barangay Halls with Day Care Centers in all Barangays, repair and renovation of the now San Juan National High School, and other public elementary schools, recreation centers like gymnasiums, basketball courts and play grounds and the creation of different livelihood centers, improvement and replacement of drainages, concreting of municipal roads and the construction of a four-storey San Juan Medical Center and the San Juan Municipal Gymnasium. During his incumbency, San Juan gained the reputation of being one of the most progressive municipalities and the Most Peaceful Municipality in the Philippines.

In 2004, he was elected as senator. During his first term, he introduced at least 617 bills and resolutions and steered the passage of at least 16 bills either as principal sponsor or principal author.

On August 15, 2007, the Supreme Court voted 13-0 to uphold the Sandiganbayan's decision to grant his bail in connection with his plunder case before the graft court. His father, former president Joseph "Erap" Estrada was the main accused in that plunder case, and was subsequently convicted. However, Erap was immediately pardoned by then Pres. Gloria Macapagal-Arroyo.[2] On September 11, 2007 Estrada introduced Senate bill 1556, proposing to make ROTC mandatory for all college students.

In 2010, he was reelected as senator, finishing in the 2nd place. During the opening of the 15th Congress on July 26, 2010, he was reelected as Senate president pro tempore.

He is presently accused of another plunder charge at the Ombudsman relating to Janet Lim Napoles' pork barrel scam involving P10 billion of the people's money. Two other senators--Juan Ponce Enrile and Bong Revilla--as well as more than 2 dozens individuals are charged with him.

In August 2010, Estrada claimed that while traveling to Hong Kong, he experienced a backlash of the emotions surrounding the death of 8 Chinese nationals from Hong Kong during the 2010 Manila hostage crisis. According to him, as he passed through the immigration desk in Hong Kong, officers threw back his passport at him after checking it.[3]

Estrada said the officer may not have known who he was because he used a "regular passport" for personal travel. He also said that he "understood the pain being felt by many Hong Kong nationals".[3]

According to Apple Daily, the Hong Kong immigration department recorded that Estrada visited Hong Kong with a diplomat passport, and that from an alleged video surveillance record, he and three other Filipinos were accompanied by staff from the Philippine embassy and had arranged to go through the privileged passage for diplomats. The immigration officer handed back the passport to the Philippines embassy staff, not to Estrada.[4]